Coming Home
by MillieMaeB
Summary: Just a short fic that was going to be a proper story and turned into a series of small scene shots. John Sheppard falls in love during his Ancient enforced excile to Earth. When the Ori reach Earth he's back in his city, forced to wait and hope that she makes her way home to him. Rated M for lang mainly, may write a sep fic for full smut! Thrown in a bit of Dean Winchester too!


Dr Alyssa Benson wrapped her hands around her coffee mug and stared out over her backyard. There was frost on the ground and her breath formed small white clouds as it hit the cool morning air. Two strong arms snaked around her waist and she pressed into the warmth at her back, shivering slightly.

"I have to go"

She nodded. "Safe trip"

He sighed in her ear. "Come with me"

"I can't, I'm needed here" She chewed on her lip in annoyance. They'd had this conversation, more than once.

"Other's can do your job"

"Not as well as me"

His breath huffed over her neck. "And modest too" He turned her and tipped her head to his face. "Please be careful. And once the Ori are done with put in for a transfer"

She dipped her eyes. "John.."

"Please Lyss?"

She nodded again.

Parting her lips under the press of his she enjoyed his quiet moan as he ran his tongue over hers. Keeping her eyes closed as he stepped back she waited until the sound of her front door closing reached her ears before opening them again.

Dr Alyssa Benson ate breakfast, showered and dressed in her uniform. She went to work, ate lunch with her colleagues and spoke with Hermoid about some repairs. She picked up take-out, ate dinner and watched a movie. Then she curled up in bed, pressed his pillow to her face and wept until sleep took over.

* * *

**Three weeks later, 1st Daedalus run to Atlantis.**

"Are you ill?"

"Um, pardon?"

"I said 'are you ill' Colonel?"

"No. Uh, why?"

"Because Princess Whateverhernameis was practically dry humping your leg and you were completely oblivious"

Lt Colonel Sheppard glared at the scientist. "That is no way to speak about our new trading partner Rodney. And I wasn't oblivious, I was merely politely ignoring it. Not that it's any of your damn business"

Dr McKay gaped at him.

"What?!"

"But she was hot"

"And?"

"Really hot, and already nearly naked"

"Drop it McKay"

"Did you decide you were gay while we were back on Earth?"

"Don't make me shoot you Rodney"

* * *

**Six weeks later, 2nd Daedalus run to Atlantis**

As the door to her quarters on board the Daedalus slid open Dr Benson was dragged inside and shoved up against the wall. She blinked into the darkness.

"Steven?"

"Very funny" He growled and shoved his tongue in her mouth, pinning her against the wall.

As he pulled her t-shirt over her head and pushed her back on the bed she eyed him as he kicked off his boots. "Are we on a deadline Colonel?"

He glared at her whilst unzipping his black fleece top, reaching for the hem of his shirt.

"Six weeks" He hissed. "Six weeks of fighting off a scarily persistent alien Princess"

He dragged his shirt over his head. "Six weeks of trying to convince McKay I haven't suddenly 'gone gay'"

He flicked open the belt on his BDU pants. "Six weeks of cold showers"

He shoved his pants and boxers off, kicking them to the side" Six we…" He looked her over. "Pants Benson"

"Oh, yes Sir"

He narrowed his gaze as she wiggled out of her pants. "Where was I?"

"Cold showers"

"Ah, right, thanks" He crawled up the bed between her legs, placing kisses along her stomach and chest. "Six weeks of my own right hand…"

His tongue ran round her nipple. She sighed. "…and terrible porn" He moved his mouth to her other nipple, sucking gently.

She pulled his head up. "You should have said. I'll make you up a private collection"

He groaned and his cock twitched against her.

She slid her legs up and around his waist. "Now, are you going to fuck me or not Colonel Sheppard?"

"Yes M'am" He growled.

* * *

**Seven weeks later, 3rd Daedalus run to Atlantis**

He watched her pull her boots on and run her hands through her hair before pulling it up into a messy bun.

"Daedalus doesn't leave 'til the morning"

"I can't stay here John"

"Why?"

She shifted, dropping her eyes. "I just can't"

He sat up, covers pooling around his waist, elbows propped on bent knees. "Lyss, sweetheart…"

"No John" She tapped her ear. "Hermoid"

He sighed as the white light of the transporter engulfed her. Then blinked as she reappeared.

Winking she threw something at him. Then she was gone.

Picking up the data stick he grinned.

"My girlfriend is awesome"

* * *

**Six weeks later, 4th Daedalus run to Atlantis**

She was laid along the top of him. Head pillowed on his chest, soft red waves tumbling over his skin. He traced light patterns across her back and dropped a kiss to the top of her head.

"It's getting late" She murmured into his chest.

He groaned and dropped his arms to the side. "Fine"

She snuggled deeper into him. "Better shut off the lights. I have an early start tomorrow"

She stretched, breaking free from his embrace. He groaned as he slid out of her.

"Morning sex is so much better with someone else"

She snorted and rolled out of bed.

He watched her pull on her uniform and shake her hair through her fingers. "Put in for the transfer"

She looked at him. "The reality doesn't always match up to the fantasy"

He rolled his eyes. "We won't know if we don't try"

She chewed her lip. "Ok"

"Ok?"

She nodded. "Next Daedalus run I won't leave on it"

He grinned at her.

"Don't say a word Sheppard" She reached to her ear. "Hermoid"

Laying back on his pillows he smiled. Six weeks then she'd be all his.

* * *

**3 months later**

Lt Colonel Sheppard dragged his hands over his face, trying to fight off the exhaustion and his currently pounding head. He flicked through the tablet in front of him and let out a low whistle. He'd had no idea how much paperwork Carter had to sift through as Commander of the Expedition.

He'd finally gotten her to take a break, eventually resorting to threatening to have Ronan stun her and carry her to her quarters if she didn't go voluntarily. She'd glared at him over her desk. "Fine, a couple of hours then it's your turn"

He'd agreed, anything to get her to sleep. He checked his watch and smiled slightly. She'd been gone four hours now.

Rolling his shoulders he tipped back in the chair and closed his eyes.

It had been nearly three months since they'd discovered they couldn't dial Earth and all attempts to contact the Daedalus had been met with nothing but static. Six weeks after the ship had left their orbit he'd sat in this office with Sam, hanging on to the hope that it would appear as usual. But there had been nothing but silence and an empty sky. Eventually he'd gone to the sparring room and had Ronan kick his arse until the Satedan had told him that was enough.

He swallowed. If only he could get rid of this sick feeling in his stomach.

"Sir!"

John jumped to his feet. Chuck was stood waving his arms in excitement.

'Oh god, please, please..'

He ran out the office. "Chuck?"

"It's the Daedalus Sir"

'Thank you, thank you'. "Put them through Chuck. And notify Carter"

"Pleasure Sir"

"Colonel Caldwell?"

"Colonel Sheppard. It's good to hear your voice"

He let out a quiet breath. "You too Sir. What the hell has been happening?"

"We'll be in transporter range in eight hours Sheppard. This needs to be done face to face"

"Shit"

"Sheppard?"

"Sorry Sir. It's been uh, a worrying time here"

"Understandable Sheppard. We'll put our foot down. The Hammond's right behind us"

"Uh ok"

"Daedalus out"

* * *

They had put their foot down. Seven hours later Lt Colonel Sheppard blinked as the bright light of the transporter disappeared revealing Colonel Caldwell and General O'Neill. He summoned up the energy for a lazy salute. "Sir's"

General O'Neill waved a hand at him. "Drop that shit Sheppard. We're all in the same boat now"

"That does not sound good Jack" Sam frowned at her old team leader and good friend.

"Believe me Carter, it's not" He gestured up towards the glass office. "Shall we?"

Sat around the briefing table John tried to stop his hands from shaking and looked over at the two men. O'Neill cleared his throat. "Three months ago the Ori arrived in Earth's orbit. There was no warning, our scanners failed to pick them up"

John closed his eyes. "Shit"

"Exactly. The first thing they did was take out both gates, leaving us stranded. The Odyssey and The Hammond were also both in orbit. They beamed out all survivors from the two gate sites and were then forced to engage in battle with the Ori ships. Quite frankly, we got our arses kicked. Jumping into hyperspace we hid out whilst making repairs and came up with a game plan. It was decided we would spend two weeks dipping in and out of Earth's orbit, beaming up any survivors we could find and taking pot shots at the Ori, then we would leave. Make our way to you. It would also allow us to intercept the Daedalus, brief them on the situation"

"When they joined us we took one last run at Earth and then hightailed it out of there. Three days into our journey The Odyssey reported problems with its hyperdrive. We dropped out of hyperspace and Dr Benson, along with Dr Marks and Dr Harper, beamed over to help identify the problem and make the repairs"

John fought the urge to vomit all over the floor. "And?"

"Dr Benson sent over all of her results from her diagnostic run to Hermoid and informed Caldwell it would take her at least another day to get it up and running again. Two hours later The Odyssey disappeared"

"Disappeared?"

Caldwell looked at him "There was no explosion Sheppard, no bits of ship floating in space. We still believe they're out there somewhere, the faulty hyperdrive bouncing them around space"

"Shit"

"John!"

He shifted. "Sorry M'am"

Sam looked at him curiously then turned to O'Neill. "So Earth?"

"Lost Carter. Those who survived have been converted, or are at least pretending to have been to stay alive. We regroup, rebuild our strength then go back. There may be something here in Pegasus that can defeat the Ori once and for all"

She nodded. "Ok. I think we all need time to deal with this, we also need to get the survivors settled, find them a place to stay. Tomorrow we start on planning the retaking of Earth"

"And the Odyssey?"

Rodney tapped his arm "I'll beam up to the Daedalus, maybe between me and the naked alien we can find something"

* * *

John jumped slightly as the other man stepped up beside him and propped his elbows on the rail, looking out over the ocean.

"Uh, Sir?"

"For God's sake Sheppard drop the Sir"

"Right, sorry uh, Caldwell"

The other Colonel sighed. "She put in for a transfer the day after we left here"

"Um.."

"I was pissed Sheppard, she's a damn good engineer. She patched up my ship, modified it, improved it, kept it in the sky. The Daedalus was her life, her baby and she was prepared to walk away from it for you"

"Shit, please.."

"She's also one of only two people who Hermoid didn't appear to want to kill"

John snorted.

"She's the best at what she does and Mitchell is a stubborn son of a bitch. He'll do whatever it takes to keep them safe and get them home. Don't give up hope yet John"

* * *

**Five million light years away**

Dean raised his hands. "Hey look man, we just need a couple of parts, just trying to get home"

The click of the safety echoed around the docking bay.

"Shit"

He flinched at the sound of a trigger being pulled. The man in front of him dropped to the floor, a surprised look permanently etched on his face.

Dean gave a sigh of relief and looked at the woman standing by the door. "Nice shot Dr Benson"

"Thanks"

He swallowed "You can probably put the gun down now"

"Right"

He slowly stepped towards her and plucked the gun from her hand, clicking on the safety. "You ok Doc?"

She blinked. "Yeah"

"Ok" He eyed her. "You got the parts?"

"Yeah"

"Right. Well then I suggest we get the hell off this planet and find you a large drink"

"Ok"

* * *

Colonel Mitchell stretched lazily and sighed. "I'd better get back on deck"

"You need rest Cam"

He looked over at his lover. "I can rest when we get to Atlantis"

Dean trailed a finger down his chest. "You're no good to any of us dead on your feet. Bates is perfectly capable of holding the fort for a few hours"

Cameron rolled out of bed. Dean sighed.

"You're a stubborn son of a bitch you know that?"

"You can talk Winchester" He watched the younger man get out of bed and raised a brow, eyes running over smooth, tanned skin. He licked his lips. "Of course I should shower first"

Dean rolled his eyes. "No more sex 'til you sleep for more than two hours straight"

"Is that so?"

"Yes" Dean glared at him and pulled on his jeans. "I'm worried about the Doc"

Cam looked up from buttoning his shirt. "Really?"

"Yeah. Don't think she's handling the whole stealing, killing people stuff too well. She's not a soldier Cam. Shit, most of them aren't"

"They'll learn to deal Dean, just like we did"

"Cameron.."

"I hate it as much as you baby but we have no choice, you know that" He wrapped his arms round him and nipped his neck. Dean hummed quietly.

"We're all gonna need so much therapy"

Cam huffed against his throat.

* * *

**Four months later**

Alyssa widened her eyes and clasped her hands together against her breasts. "Please don't hurt me. I'm just so hungry. I've been lost for so long"

The guard ran his eyes over her. "You all alone out here?"

She resisted the urge to roll her eyes. Men were all the same, no matter what galaxy they came from. She allowed her eyes to moisten and nodded. "Yes" She whispered.

"Well then, let's go find you some food"

"Oh thank you, how ever will I repay you?"

"Don't you worry about that for now" He grasped her elbow and led her inside.

In the shadows Dean looked at Cam and rolled his eyes. The other man grinned. Easy pickings.

Two hours later and safely back aboard the Odyssey Dr Benson looked at their haul. She furrowed her brow.

"I'm pretty sure I'm a space pirate"

Mitchell snorted. "And a kick arse one at that Princess"

* * *

Teyla laid a hand on his arm. "John?"

"Hey Tey, everything ok?"

"I am well. However I am concerned for you"

"Me?"

She sighed. "John, you must speak of your fears otherwise they will never leave you"

"Maybe I don't want them to leave yet"

"I am so sorry John. You have had something special cruelly snatched from you. It will take time"

"How much time Teyla? How long do I wait?"

"There is another?"

"No" He sighed. "Not sure if there ever will be"

"You will know here" She lay a hand on his chest. "When it is time"

"Yeah" He took a sip of tea. "I really miss sex though. Ow!"

She glared at him. "Then work on your meditation"

"Meditating sucks. And isn't nearly as fun as sex. Ow!"

He rubbed the back of his head. "Stop doing that"

"Stop thinking with your penis"

He gaped at her.

* * *

**One month later**

"This is Colonel Mitchell, Commander of Atlantis"

"Bollocks. It's the wrong one again"

"Uh..please identify yourselves"

A woman's voice drifted through the gateroom. "Do you have a Lt Colonel John Sheppard as Military Commander?"

"Uh, we have a Full Bird Colonel John Sheppard"

"Cool. Is he single?"

"Uh, excuse me?"

"Lyss!" A vaguely familiar voice floated over the radio. "We are not alternate reality jumping just for you to get laid"

"So not fair"

The other voice cleared its throat. "Uh, sorry about that. Probably best you forget this conversation"

"Who the hell are you people?!"

There was an excited squeal. "He sounds just like him!"

"No Alyssa"

"It's alright for you Cameron, you're having lovely gay sex. I've had to make do with my right hand for the past eight months"

"Jesus woman, will you cut it out. Uh, like I said, probably best to forget we were ever here. Uh, good luck and all that"

The transmission cut out.

Full Bird Colonel Sheppard and Full Bird Colonel Mitchell looked at each other.

"I'm not gay"

Colonel Sheppard pouted. "But I'm single and she sounded hot" He looked thoughtful. "Do we have an Alyssa among the personnel?"

* * *

"Major"

"Sir"

"Is there something I can do for you Lorne?"

"Uh, I was just wondering why you're hiding in a storage cupboard Sir"

"I'm not hiding Major"

"Ok"

"I'm tactically retreating"

Evan raised a brow.

"Uh, Sergeant Crawford…"

"Ah"

"Yeah" He shifted a little. "It was either this or a cold shower and a stiff drink"

"Ah" Lorne studied the ceiling. "Would you like me to, uh, take over Sir?"

"I knew there was a reason I hadn't shot you yet Major"

"Thank you Sir. Permission to take the next twenty-eight hours off Sir"

"Twenty-eight! Are you sure?"

"I believe in performing my duties to the best of my ability Sir"

"You're a whore Major"

"Thank you Sir"

* * *

**Three weeks later**

"Do you have a Lt Colonel John Sheppard as Military Commander?" The voice sounded bored.

"Lyss?!"

"John?! Oh my God, shit! Cameron wake up! It's our Atlantis! Cameron!"

"Uh, Lyss?"

"John, listen to me. You need to get McKay to…"

"Lyss? I need to get McKay to do what? Lyss? Lyssa?!"

Static.

"Sorry Sir, they've gone"

"Fuck!"

* * *

"Fuck! Stupid fucking reality jumping pile of shit" She kicked the console.

"Hey! No kicking my ship!"

"Your ship sucks arse! The Daedalus was so much better!"

"Off my bridge, now!"

She left, muttering to herself.

Mitchell glared at a grinning Major Womak. "Bring us to a stop. Let's see if our resident genius can get us back there"

"Yes Sir"

Dean jogged onto the bridge, followed by his brother. "Just seen Doc. Her language has really gone downhill. Think we're a bad influence"

Sam snorted.

"Bite me Winchester"

* * *

**One month and one week later**

Major John Sheppard opened his eyes and looked around his tent. She was gone.

She hadn't given her name but she was beautiful and willing. And he'd been too damn lonely for too long.

He frowned into the darkness. He hadn't given his name either but when she'd whispered it as she came the love and pain wrapped up in that one word had sent shivers up his spine.

* * *

He found her curled in front of the terminal she'd been working on, silent tears running down her face.

"Princess?" He whispered. "What's wrong?"

Her body shuddered. "I can't do this anymore Cameron"

He closed his eyes, pushing back his own despair. "Yes you can. You're stronger than you think"

"No I'm not. I..I don't think I could even look him in the eye anymore. Even if by some miracle we made it back. I'm…I'm not who he fell in love with"

He dropped into a crouch by her side and brushed her tears away. "Yes you are Alyssa, and so much more. If he doesn't want you after all you've done to get back to him then he's a prick and doesn't deserve you"

She shook her head. "I don't deserve him, not anymore"

* * *

"McKay?"

"I'm sorry John. I've gone over everything. There's nothing we can do to get them back here. It's all up to them"

"Shit"

The scientist pointed at him. "BUT…"

John raised his brows.

"Next time they appear I know what she needs me to do"

"Thank you Rodney"

"Uh, John?"

"Yes?"

"Please stop hugging me, you're freaking me out"

Colonel Carter snorted.

* * *

**One month later**

"Atlantis, this is Colonel Cameron Mitchell of The Odyssey. Do you read?"

"Colonel Mitchell, it's good to have you back…again"

"Good to be back Sam, hear a friendly voice. We don't have much time"

"Dr McKay knows what to do. Hang on Cam"

"Hanging on with both hands Sam"

* * *

Lt Colonel John Sheppard wearily stepped through the gate and rolled his shoulders. Sergeant Crawford was starting to look tempting. He looked up and blinked, mouth dropping open.

"Shep, good to see you"

He stared at the man standing next to Sam.

"John? You ok?"

"You're back"

"Yep"

"Shit"

Colonel Mitchell grinned at him. "Still as eloquent as ever Colonel Sheppard"

"Shit"

* * *

He found her buried up to her waist in a console.

"Lyss?"

Her movements stilled. "There's a reason I was staying up here" Her voice was muffled.

"And that was?"

"You're supposed to be busy. You know briefings and shit"

He raised his brows. "And shit?"

Silence.

"Lyss will you please come out from there?"

"Busy"

"Alyssa Benson don't make me drag you out of there by your feet"

He had no idea how big the console was but she seemed to disappear even further into it.

"Out here now Dr Benson"

"Please go away Colonel"

He folded his arms across his chest. "No"

He heard a soft sigh then she wriggled back, eventually standing in front of him.

"What?"

"What?! That's all I get? It's been nearly a year sweetheart"

"Seems longer. And don't call me sweetheart"

He narrowed his gaze. "What the fuck is going on?"

* * *

**Two months later**

Dean dropped down beside Colonel Mitchell and looked into the flames. "Who knew going off-world didn't have to involve being shot at or aggressively groped by alien natives"

Mitchell growled. "Groped?"

He chuckled. "Don't worry baby, I told them I was taken"

"You better fucking have"

"You know you're hot when you get all possessive" He ran his tongue up his lovers neck.

"Cut it out Winchester. We're expected to stay for at least another hour"

Dean huffed then raised his brows. "I see the Doc has made a new friend" He eyed her through the fire as she took a gulp of her drink and laughed at something the man next to her had said.

"Leave her be Dean"

"Really? For fuck's sake Cam what the hell is wrong with her? She should be back in the city with Colonel Broody"

Cam snorted. "Stop calling him that baby. He'll shoot you for it one day and then I'll have to kill him"

Dean hummed and ran a finger up the seam of his BDU pants. Cam growled. "I told you to cut it out"

"Yeah, yeah, ok. So, what is her problem? She practically spent the whole time we were gone mooning over him"

Cam sighed. "You remember about a month after we'd got to Atlantis the first time and we didn't think we'd get back?"

"Yeah"

"She ran into that reality's Sheppard"

"Ah"

"I found her after, she said she didn't deserve him anymore"

"Shit"

"Yeah"

"Baby?"

"Yeah?"

"He thinks one of us is fucking her"

Colonel Mitchell spat our his drink. "What?!"

"We've all gotten pretty close Cam and I'm sure none of them know about us. Except O'Neill, the man knows everything"

Cam grinned. "Yeah. Ok, shit, what do we do?"

"I think it's time Colonel Broody knew exactly what went down while we were away"

"Stop calling him that!"

* * *

**Two weeks later**

Lt Colonel Sheppard eyed the man who'd dropped into the seat opposite him.

"Mitchell"

"Sheppard"

He shifted. "Something I can help you with Colonel?"

"Can't I join an old friend for lunch?"

"Ok" John ran his eyes over the table where she sat.

"Beautiful, isn't he?"

"Um, excuse me?"

"Dean. I'm a fucking lucky bastard"

"Uh.."

The man opposite him sighed. "Jesus Shep, what happened to your black op skills. I'm fucking the man"

John spat out his coffee. "What?!"

"I..am..fucking..Dean..Winchester" Cam rolled his eyes. "Have been since a month after we left Earth"

"Jesus Cam, you want to keep it down"

"Hey, I've got nothing to worry about. Earth's gone, along with the regs. Also I happen to know that O'Neill is practically married to Jackson"

John closed his eyes. "Fuck Mitchell, what the hell happened to you?"

"I got stranded in deep space with a possibility of never getting home Shep. Makes you see sense, realise what's really important"

He flicked a glance over at her and sighed. "Yeah, I guess so"

"John?"

"What Mitchell? You gonna tell me you're in a three-way with a wookie or something"

"Stop being a sarcastic bastard"

John glared at his friend.

"Listen up Shep. And this stays between me and you cause she'll kick my arse if she finds out"

"SHE'LL kick YOUR arse?"

Colonel Mitchell chuckled. "We were gone a long time John, she had to step up. Dean and his brother pretty much taught her how to whale on anyone"

He raised his brows.

"She killed, and she stole, and she conned her way round the whole fucking universe to get back to you John. And now she's punishing herself for one little slip up, one moment of weakness in eleven months. If you can forgive her for that then maybe she will"

"Slip up?"

"Talk to her John"

* * *

She didn't look up from her tablet. "Is there something I can help you with Colonel Sheppard?"

He rolled his eyes and took the tablet out of her hands.

"Hey! What the fuck?"

He propped himself against the work table. "Your language has become a lot more colourful since you were gone"

She glared at him. "Is that all?"

"No, it fucking well isn't"

"Excuse me?"

"Why did you really change your mind about us?"

"I told you already, stop being a girl about it"

He growled. "You were lying"

"Was not"

"Was too"

"Wa…shit, this is ridiculous. Just drop it John"

"No"

* * *

**One week later**

Dr Benson grit her teeth and tried to ignore the man sprawled on the couch in her lab. He was reading War and Peace. This was the seventh night in a row.

He started humming quietly.

"Right, fine!" She stood up. "You win! I ended it because I had sex with another version of you. Satisfied?!"

She turned and stalked out, not looking at his face.

* * *

"That's the only reason?"

She closed her eyes.

"Why can't you just leave me alone?"

"Because I love you"

She gripped the railings.

"So in eleven months you gave in once, sought out a bit of comfort. If another version of you had shown up here I probably wouldn't have been able to keep it in my pants either"

"John…"

"You're finally here Lyss, even if it happened in the shittiest way possible. Come back to me, please"

* * *

**One year later**

The door to their quarters slid open and she stepped inside.

"I am a fucking genius"

He snorted. "Is that so Dr Sheppard?"

"Uh huh" She dropped into his lap. "We're gonna kick the Ori's pale creepy arses"

"All thanks to you?" He traced slick swirls over her throat.

She squirmed in his grasp. "Yep. Well, maybe McKay helped a little"

"Really?" His hand slid up under her shirt.

"Umhmm"

"And what have you two geniuses come up with?" His thumb ghosted over her nipple.

She slid her eyes shut and tipped back her head. "A really big honking space gun"

"I knew there was a reason I married you"


End file.
